Abstract: The objectives of the sustainable development of the aquaculture industry involve promoting green ecological aquaculture, scientifically grasping the spatial correlation network structure of freshwater aquaculture carbon emission efficiency, and laying the foundation for the development of low-carbon transformation of agriculture. To develop a more scientific aquaculture program, improve the efficiency of resource use, and reduce damage to the environment, this study investigated the carbon emission efficiency of freshwater aquaculture in China from a spatial correlation perspective, taking 30 provinces and cities in China as the research object from 2008 to 2021, measured the carbon emission efficiency of freshwater aquaculture using the Super-Slacks Based Measurement (SBM) model, analyzed the characteristics of its spatial correlation network structure on the basis of the modified gravitational model and social network analysis, and analyzed the influencing factors empirically using the Quadratic Assignment Procedure model. The results showed that the spatial and temporal distribution of the carbon emission efficiency of freshwater aquaculture in China was uneven, with a fluctuating upward trend over time and a decreasing gap between regions in space. The strength of the spatial linkage gradually increased, but it was still far from the ideal state; the overall network correlation also increased, and the structure was relatively stable. The eastern coastal region has always been in a dominant position in the spatial network and has a significant impact on the spatial correlation of carbon emission efficiency, while the northwestern, southwestern and northeastern regions are in a subordinate position in the network and have a weak impact on the spatial correlation of carbon emission efficiency, and some provinces and municipalities in the central region play the roles of “bridges” and “intermediaries”. The optimization of aquaculture species structure and the improvement of freshwater aquaculture technology can promote cooperation and exchange between aquaculture regions and facilitate the formation of spatial linkage networks. Carbon sinks are important for ecological protection and governance, and the construction of infrastructure improves the conditions of regional transportation and communication, which makes the inter-regional links convenient and close and promotes the formation of spatial linkage networks. The increase in aquaculture density will lead to the deterioration of the aquaculture environment, which is not conducive to the sustainable development of the industry, and the economic development of the fishery industry has a positive but insignificant impact on the formation of spatial connectivity networks. To develop green and low-carbon aquaculture and enhance the carbon emission efficiency of freshwater aquaculture, regional synergistic development policies, optimization of the structure of aquaculture species, and upgradation of aquaculture technology should be formulated according to local conditions. Emphasis should be placed on low-carbon emission reduction resources between different provinces, regional linkages in carbon emission efficiency of freshwater aquaculture should be promoted, and similarities in aquaculture densities should be used to mobilize regional assimilation effects and further narrow the gap between regions.